From 4230206ab4f69b110a9730ca150a56d123efd7ee Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 17 Sep 2018 10:21:28 +0200
Subject: [PATCH] Make bamIndexPath required
---
samtools.wdl | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/samtools.wdl b/samtools.wdl
index ab2c84e..8bdf771 100644
--- a/samtools.wdl
+++ b/samtools.wdl
@@ -26,7 +26,7 @@ task Index {
input {
String? preCommand
File bamFile
- String? bamIndexPath
+ String bamIndexPath
}
command {
@@ -38,7 +38,7 @@ task Index {
output {
IndexedBamFile outputBam = object {
file: bamFile,
- index: select_first(flatten([[bamIndexPath], glob(sub(basename(bamFile), "\.bam$", "") + "*.bai")]))
+ index: bamIndexPath
}
}
}
--
GitLab